The Cats were trailing Hawthorn by 21 points in the first quarter of Friday night's game at the MCG when Mabior Chol tackled Stewart in Geelong's defensive 50.
Stewart, who was also clutching his right wrist, needed immediate treatment and was assisted to the bench before being ruled out of the game through concussion and replaced by substitute Jhye Clark.
It means if the Cats make the grand final, they will be without brilliant premiership defender Stewart due to the AFL's 12-day concussion protocols.
Because Chol pinned both arms and went into Stewart's back, he could also face scrutiny from the match review officer.
The change forced fellow defender Jack Henry, who was on the bench after being treated for an ankle injury, to return to the fray to cover for Stewart.
Henry was injured earlier in the first quarter when teammate Connor O'Sullivan landed on his left ankle.
He was assisted from the field by two trainers, without putting any weight on the questionable ankle, then had to go to the rooms for treatment.
Henry returned to play with the ankle heavily strapped and looking noticeably proppy, when Stewart left the field.
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